Standard fit report for fits of SISCA to HG_Herring data.
Data Scenario: setup_HG
Model Hypothesis: setup_Aggregate_AR1comps
Species:
Stocks:
Max Gradient: 0.004894
Objective Function value: 181.6675153
Time to fit model: 0.05
PD Hessian: FALSE
No. of Non-finite SEs: 0
Figure 1: Time series of spawning biomass with scaled spawn indices (top), recruitments (second row), natural mortality (third row), and harvest rates (bottom row) for substocks of HG_Herring. Stocks are, from left to right,Aggregate.
Figure 2: Model fits to spawn indices.
Figure 3: Average model fits to age data. Stocks are left to right, and gears are top to bottom.
Figure 4: Model fits to age data, averaged over stock and time. Gears are top to bottom.
| \(\tau^{age}_{Red}\) | \(\tau^{age}_{SR}\) | \(\tau^{age}_{Gn}\) | \(\tau^{surv}_{Su}\) | \(\tau^{surv}_{D}\) | |
|---|---|---|---|---|---|
| Aggregate | 0.823 | 0.434 | 0.649 | 0.466 | 0.479 |
Figure 5: Age-1 recruitments for all stocks. Equilibrium unfished recruitment \(R_0\) is indicated by the horizontal dashed line. Second row shows recruitment residuals on the log scale, with the average of estimated residuals shown by the horizontal red dashed line.
Figure 6: Stock-recruit curves (solid lines) and modeled recruitments (coloured points)
Figure 7: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 8: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 9: Selectivity-at-age for each fleet (rows). Aggregate stock average selectivity curves are shown as thick grey lines, while sub-stock specific estimates are shown as dashed thin coloured lines.
Figure 10: Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the gillnet fleet.
Figure 11: Model fits to yearly Aggregate stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 12: Model fits to yearly Aggregate stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 13: Model fits to yearly Aggregate stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 14: Age composition residuals for the Aggregate sub-stock. Positive residuals are black black, while negative residuals are red.
Figure 15: Model fits to tail compressed yearly Aggregate stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 16: Model fits to tail compressed yearly Aggregate stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 17: Model fits to tail compressed yearly Aggregate stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
| objFun | obsSurface | obsDive | ageRed | ageSR | ageGill | |
|---|---|---|---|---|---|---|
| Total | 181.67 | -10.48 | -6.11 | 19.86 | -26 | 7.42 |
| Aggregate | 181.67 | -10.48 | -6.11 | 19.86 | -26 | 7.42 |
| V1 | |
|---|---|
| objFun | 181.670000 |
| recDevs | 86.320000 |
| initDevs | 9.970000 |
| h | 7.930000 |
| M | 1.090000 |
| tvMdev | 67.370000 |
| IGtau_surf | -4.130000 |
| IGtau_dive | -4.210000 |
| tvSelAlpha | 0.000000 |
| tvSelBeta | 0.000000 |
| selAlphaRed | 2.850000 |
| selAlphaSR | 2.850000 |
| selAlphaGn | -0.690000 |
| selBetaRed | -1.290000 |
| selBetaSR | -1.290000 |
| selBetaGn | -0.440000 |
| lnB0 | 3.243168 |
| lnRinit | 5.778798 |
| psiSOK | -20.390000 |
| V1 | |
|---|---|
| objFun | 181.67 |
| MDev | 0.92 |
| hDev | 0.92 |
| selAlphaDevR | 0.92 |
| selAlphaDevSR | 0.92 |
| selAlphaDevGn | 0.92 |
| selBetaDevR | 0.92 |
| selBetaDevSR | 0.92 |
| selBetaDevGn | 0.92 |
| phase | objFun | maxGrad | nPar | convCode | convMsg | time |
|---|---|---|---|---|---|---|
| 1 | 545.6249 | 0.0000657 | 3 | 0 | relative convergence (4) | 0.0061167 |
| 2 | 544.5749 | 0.0000884 | 13 | 0 | relative convergence (4) | 0.0040667 |
| 3 | 472.7940 | 0.0000726 | 81 | 0 | relative convergence (4) | 0.0043000 |
| 4 | 269.6006 | 0.0001420 | 146 | 0 | relative convergence (4) | 0.0060833 |
| 5 | 269.6006 | 0.0000722 | 146 | 0 | relative convergence (4) | 0.0040000 |
| 6 | 265.4987 | 0.0005303 | 150 | 0 | relative convergence (4) | 0.0068333 |
| 7 | 263.7022 | 0.0006852 | 153 | 0 | relative convergence (4) | 0.0070333 |
| 8 | 263.7022 | 0.0003487 | 153 | 0 | relative convergence (4) | 0.0040833 |
| 9 | 181.6675 | 0.0048940 | 155 | 0 | relative convergence (4) | 0.0097167 |
| RE | NA | NA | NA | NA | NA | NA |
| est | se | gr | cv | |
|---|---|---|---|---|
| lnB0_p | 3.2432 | 0.0689 | -0.007 | 0.0212 |
| lnRinit_p | 5.7788 | 0.4169 | -0.0023 | 0.0721 |
| logit_ySteepness | 0.4934 | 0.6099 | 2.4e-05 | 1.2362 |
| lnM | -1.3882 | 0.2348 | 0.00073 | 0.1691 |
| fDevs_ap | 0.9699 | 0.6562 | -0.00076 | 0.6765 |
| fDevs_ap.1 | -0.2549 | 0.6631 | -0.00029 | 2.6016 |
| fDevs_ap.2 | 0.3603 | 0.6386 | -0.00041 | 1.7727 |
| fDevs_ap.3 | 0.4762 | 0.6439 | -0.00027 | 1.3522 |
| fDevs_ap.4 | 0.0695 | 0.6787 | -8.1e-05 | 9.7619 |
| fDevs_ap.5 | 0.0473 | 0.7209 | -6.6e-05 | 15.2285 |
| fDevs_ap.6 | -0.3239 | 0.8697 | -3.7e-05 | 2.6854 |
| fDevs_ap.7 | -0.2021 | 0.9166 | -2.3e-05 | 4.5361 |
| fDevs_ap.8 | -0.1283 | 0.9468 | -1.6e-05 | 7.3823 |
| fDevs_ap.9 | -0.1542 | 0.9360 | -2.2e-05 | 6.0702 |
| lnSelAlpha_g | 1.0174 | 0.0649 | 0.00077 | 0.0638 |
| lnSelAlpha_g.1 | 1.3489 | 0.0430 | 0.0026 | 0.0318 |
| lnSelAlpha_g.2 | 1.6499 | 0.0430 | -0.017 | 0.026 |
| lnSelBeta_g | 0.6489 | 0.1014 | 0.00024 | 0.1563 |
| lnSelBeta_g.1 | 0.6024 | 0.0719 | 0.00013 | 0.1193 |
| lnSelBeta_g.2 | 0.2647 | 0.1144 | 0.006 | 0.4324 |
| lntau2Obs_pg | -1.5292 | 0.1973 | 4.1e-05 | 0.129 |
| lntau2Obs_pg.1 | -1.4707 | 0.2057 | -2.7e-05 | 0.1399 |
| recDevs_vec | 1.2917 | 0.4671 | -0.0018 | 0.3616 |
| recDevs_vec.1 | -1.0435 | 0.7785 | -0.00022 | 0.7461 |
| recDevs_vec.2 | -0.4390 | 0.4125 | -0.00031 | 0.9395 |
| recDevs_vec.3 | -0.7076 | 0.4533 | -0.00017 | 0.6407 |
| recDevs_vec.4 | 0.9106 | 0.3662 | -0.00047 | 0.4021 |
| recDevs_vec.5 | -0.0792 | 0.8295 | -0.00014 | 10.4752 |
| recDevs_vec.6 | 0.2288 | 0.6790 | -0.00024 | 2.9673 |
| recDevs_vec.7 | 0.3971 | 0.6073 | -0.00035 | 1.5295 |
| recDevs_vec.8 | 0.0534 | 0.7658 | -0.00028 | 14.3465 |
| recDevs_vec.9 | 1.1614 | 0.5920 | -0.00084 | 0.5097 |
| recDevs_vec.10 | 0.3537 | 0.7053 | -0.00035 | 1.994 |
| recDevs_vec.11 | -0.9393 | 0.7045 | -3.9e-05 | 0.75 |
| recDevs_vec.12 | -1.6066 | 0.6703 | 2.6e-06 | 0.4172 |
| recDevs_vec.13 | -1.2781 | 0.6782 | -4.9e-05 | 0.5306 |
| recDevs_vec.14 | -0.4707 | 0.5245 | -6.6e-05 | 1.1143 |
| recDevs_vec.15 | -0.0392 | 0.5211 | -2.9e-06 | 13.2795 |
| recDevs_vec.16 | 0.6240 | 0.4025 | -5e-05 | 0.645 |
| recDevs_vec.17 | 0.4506 | 0.3420 | -5.3e-05 | 0.759 |
| recDevs_vec.18 | 1.1650 | 0.2649 | -0.00017 | 0.2274 |
| recDevs_vec.19 | 1.0518 | 0.2626 | -0.00044 | 0.2497 |
| recDevs_vec.20 | 1.1527 | 0.2561 | -0.00074 | 0.2221 |
| recDevs_vec.21 | -0.4422 | 0.3074 | 0.002 | 0.6951 |
| recDevs_vec.22 | -0.2750 | 0.3260 | -0.0019 | 1.1855 |
| recDevs_vec.23 | 0.2173 | 0.3191 | 0.00057 | 1.4682 |
| recDevs_vec.24 | -0.3331 | 0.3159 | -1.9e-05 | 0.9483 |
| recDevs_vec.25 | 2.7452 | 0.2772 | 0.0017 | 0.101 |
| recDevs_vec.26 | 0.5333 | 0.2779 | -0.00017 | 0.5211 |
| recDevs_vec.27 | -0.5640 | 0.2850 | 0.00023 | 0.5053 |
| recDevs_vec.28 | -0.7854 | 0.2923 | -0.00031 | 0.3721 |
| recDevs_vec.29 | 1.2643 | 0.2751 | -0.00074 | 0.2176 |
| recDevs_vec.30 | 0.4142 | 0.2761 | -0.00057 | 0.6665 |
| recDevs_vec.31 | -1.1791 | 0.3055 | -0.00057 | 0.2591 |
| recDevs_vec.32 | -0.7794 | 0.2671 | -0.00039 | 0.3427 |
| recDevs_vec.33 | 1.5860 | 0.2381 | -0.00057 | 0.1501 |
| recDevs_vec.34 | 0.5273 | 0.2387 | 0.00097 | 0.4527 |
| recDevs_vec.35 | -0.3701 | 0.2474 | 0.00035 | 0.6684 |
| recDevs_vec.36 | -1.4279 | 0.2837 | 4.4e-05 | 0.1987 |
| recDevs_vec.37 | 0.5952 | 0.2617 | 1e-05 | 0.4396 |
| recDevs_vec.38 | -1.9407 | 0.3582 | -4e-06 | 0.1846 |
| recDevs_vec.39 | -1.9846 | 0.3652 | -0.00025 | 0.184 |
| recDevs_vec.40 | -1.1449 | 0.3459 | -0.00021 | 0.3021 |
| recDevs_vec.41 | 0.1271 | 0.2789 | -1.5e-06 | 2.1943 |
| recDevs_vec.42 | 0.4162 | 0.2792 | -9.2e-06 | 0.6708 |
| recDevs_vec.43 | 1.4833 | 0.2481 | 0.00038 | 0.1672 |
| recDevs_vec.44 | -1.7064 | 0.3059 | 2.1e-05 | 0.1793 |
| recDevs_vec.45 | -0.5300 | 0.2922 | 3e-05 | 0.5513 |
| recDevs_vec.46 | -0.5396 | 0.3010 | -1.7e-05 | 0.5578 |
| recDevs_vec.47 | -0.3611 | 0.3008 | 1.6e-05 | 0.8331 |
| recDevs_vec.48 | 0.8038 | 0.2912 | 5e-05 | 0.3623 |
| recDevs_vec.49 | -0.8037 | 0.4114 | 1.9e-07 | 0.5119 |
| recDevs_vec.50 | 0.4915 | 0.3695 | 2.1e-05 | 0.7518 |
| recDevs_vec.51 | -0.8347 | 0.4463 | 6.7e-06 | 0.5347 |
| recDevs_vec.52 | 0.7378 | 0.3888 | -1.1e-05 | 0.527 |
| recDevs_vec.53 | -0.9491 | 0.3941 | -1.9e-05 | 0.4153 |
| recDevs_vec.54 | 0.7795 | 0.3463 | 4.2e-06 | 0.4442 |
| recDevs_vec.55 | -1.1963 | 0.4211 | -1.5e-05 | 0.352 |
| recDevs_vec.56 | 0.2639 | 0.3512 | -2e-05 | 1.3309 |
| recDevs_vec.57 | -0.3555 | 0.3708 | -2.5e-05 | 1.0431 |
| recDevs_vec.58 | 1.2523 | 0.3132 | -2.5e-05 | 0.2501 |
| recDevs_vec.59 | -0.9032 | 0.3891 | -3.5e-05 | 0.4308 |
| recDevs_vec.60 | -0.5239 | 0.3840 | 1.3e-06 | 0.7329 |
| recDevs_vec.61 | -1.0686 | 0.3875 | -1.7e-05 | 0.3626 |
| omegaM_pt | -0.3739 | 0.9796 | 4.6e-05 | 2.6201 |
| omegaM_pt.1 | -0.3745 | 0.9775 | 5.5e-06 | 2.6101 |
| omegaM_pt.2 | -0.1125 | 0.9738 | -3.3e-05 | 8.6567 |
| omegaM_pt.3 | 0.1813 | 0.9707 | -0.00012 | 5.354 |
| omegaM_pt.4 | 0.4342 | 0.9708 | -0.00021 | 2.2359 |
| omegaM_pt.5 | 0.7556 | 0.9728 | -3e-04 | 1.2874 |
| omegaM_pt.6 | 0.6511 | 0.9711 | -0.00032 | 1.4915 |
| omegaM_pt.7 | 0.5926 | 0.9699 | -0.00033 | 1.6365 |
| omegaM_pt.8 | 0.6635 | 0.9705 | -0.00034 | 1.4626 |
| omegaM_pt.9 | 0.6213 | 0.9714 | -0.00035 | 1.5634 |
| omegaM_pt.10 | 0.5794 | 0.9715 | -0.00038 | 1.6768 |
| omegaM_pt.11 | 0.5128 | 0.9698 | -0.00041 | 1.8911 |
| omegaM_pt.12 | 0.5810 | 0.9655 | -0.00048 | 1.6619 |
| omegaM_pt.13 | 0.6814 | 0.9638 | -0.00055 | 1.4144 |
| omegaM_pt.14 | 0.7708 | 0.9629 | -0.00058 | 1.2493 |
| omegaM_pt.15 | 0.5379 | 0.9670 | -0.00057 | 1.7978 |
| omegaM_pt.16 | 0.1391 | 0.9712 | -0.00056 | 6.9835 |
| omegaM_pt.17 | -0.0843 | 0.9709 | -0.00055 | 11.5124 |
| omegaM_pt.18 | -0.1292 | 0.9658 | -0.00054 | 7.4749 |
| omegaM_pt.19 | -0.0974 | 0.9618 | -0.00053 | 9.8748 |
| omegaM_pt.20 | -0.1361 | 0.9604 | -0.00052 | 7.0585 |
| omegaM_pt.21 | -0.2982 | 0.9582 | -0.00052 | 3.2136 |
| omegaM_pt.22 | -0.3715 | 0.9527 | -0.00054 | 2.5643 |
| omegaM_pt.23 | -0.2379 | 0.9458 | -6e-04 | 3.9763 |
| omegaM_pt.24 | -0.1186 | 0.9414 | -0.00055 | 7.9371 |
| omegaM_pt.25 | 0.0567 | 0.9386 | -6e-04 | 16.5399 |
| omegaM_pt.26 | 0.2101 | 0.9372 | -0.00061 | 4.4598 |
| omegaM_pt.27 | 0.2440 | 0.9356 | -0.00062 | 3.8343 |
| omegaM_pt.28 | 0.2380 | 0.9363 | -0.00054 | 3.9338 |
| omegaM_pt.29 | 0.2844 | 0.9381 | -0.00046 | 3.2985 |
| omegaM_pt.30 | 0.3004 | 0.9388 | -0.00037 | 3.1257 |
| omegaM_pt.31 | 0.3651 | 0.9376 | -3e-04 | 2.568 |
| omegaM_pt.32 | 0.4621 | 0.9360 | -0.00027 | 2.0258 |
| omegaM_pt.33 | 0.5172 | 0.9355 | -0.00028 | 1.8086 |
| omegaM_pt.34 | 0.3741 | 0.9349 | -0.00033 | 2.4991 |
| omegaM_pt.35 | 0.0488 | 0.9354 | -0.00041 | 19.1766 |
| omegaM_pt.36 | -0.0319 | 0.9343 | -0.00054 | 29.28 |
| omegaM_pt.37 | -0.1160 | 0.9344 | -0.00059 | 8.0586 |
| omegaM_pt.38 | 0.0912 | 0.9288 | -0.00061 | 10.1801 |
| omegaM_pt.39 | 0.3082 | 0.9229 | -0.00063 | 2.9941 |
| omegaM_pt.40 | 0.4321 | 0.9249 | -0.00061 | 2.1405 |
| omegaM_pt.41 | 0.4174 | 0.9266 | -0.00059 | 2.2199 |
| omegaM_pt.42 | 0.3860 | 0.9246 | -0.00058 | 2.3956 |
| omegaM_pt.43 | 0.3878 | 0.9254 | -0.00059 | 2.3864 |
| omegaM_pt.44 | 0.1616 | 0.9281 | -6e-04 | 5.7429 |
| omegaM_pt.45 | 0.1011 | 0.9279 | -0.00062 | 9.1776 |
| omegaM_pt.46 | 0.3095 | 0.9232 | -0.00061 | 2.9827 |
| omegaM_pt.47 | 0.5056 | 0.9179 | -6e-04 | 1.8154 |
| omegaM_pt.48 | 0.5623 | 0.9133 | -0.00057 | 1.6242 |
| omegaM_pt.49 | 0.5736 | 0.9145 | -0.00055 | 1.5943 |
| omegaM_pt.50 | 0.5133 | 0.9240 | -0.00052 | 1.8001 |
| omegaM_pt.51 | 0.0807 | 0.9259 | -0.00049 | 11.4674 |
| omegaM_pt.52 | -0.0429 | 0.9265 | -0.00046 | 21.6181 |
| omegaM_pt.53 | -0.1666 | 0.9252 | -0.00043 | 5.5522 |
| omegaM_pt.54 | -0.4362 | 0.9279 | -4e-04 | 2.1271 |
| omegaM_pt.55 | -0.3965 | 0.9267 | -0.00037 | 2.3369 |
| omegaM_pt.56 | -0.3570 | 0.9279 | -0.00034 | 2.5994 |
| omegaM_pt.57 | -0.3126 | 0.9281 | -0.00031 | 2.9691 |
| omegaM_pt.58 | -0.2143 | 0.9282 | -0.00028 | 4.331 |
| omegaM_pt.59 | -0.1416 | 0.9272 | -0.00025 | 6.5495 |
| omegaM_pt.60 | -0.0915 | 0.9267 | -0.00023 | 10.1317 |
| omegaM_pt.61 | 0.1025 | 0.9269 | -2e-04 | 9.0451 |
| omegaM_pt.62 | 0.2726 | 0.9301 | -0.00018 | 3.4127 |
| omegaM_pt.63 | 0.3991 | 0.9357 | -0.00015 | 2.3442 |
| omegaM_pt.64 | 0.5263 | 0.9323 | -0.00012 | 1.7714 |
| omegaM_pt.65 | 0.0897 | 0.9487 | -9.1e-05 | 10.5778 |
| omegaM_pt.66 | -0.1325 | 0.9699 | -5.9e-05 | 7.3188 |
| omegaM_pt.67 | -0.1939 | 0.9841 | -2.9e-05 | 5.0752 |
| logitphi1_g | -1.0070 | 0.5812 | -2.2e-05 | 0.5772 |
| logitphi1_g.1 | 0.5791 | 0.2386 | 2.4e-05 | 0.412 |
| logitphi1_g.2 | 0.6935 | 0.4428 | -0.0058 | 0.6384 |
## Not Yet Implemented
Figure 18: Estimated correlation matrices for age composition residuals in the reduction fleet. The circles above the visualise the numbers below the diagonal.
Figure 19: Estimated correlation matrices for age composition residuals in the seineRoe fleet. The circles above the visualise the numbers below the diagonal.
Figure 20: Estimated correlation matrices for age composition residuals in the gillnet fleet. The circles above the visualise the numbers below the diagonal.
Figure 21: Diagnostic plot for compositional likelihood function.
Figure 22: Plots of average age composition fits at the major stock level. Left is SISCA, right is ISCAM.
Figure 23: Comparison of spawning stock biomass and age-2 recruitment at the major stock level between ISCAM and SISCA.